Analysis of any point mutation in DNA. The amplification refractory mutation system (ARMS)

HLA-A locus DNA typing of the 4AOH cell panel by arms PCR

As part of the Fourth Asia-Oceania Histocompatibility (4AOH) Workshop, the authors have demonstrated a method of DNA-based tissue typing of the HLA-A locus using ARMS-designed primers in a panel of specific PCR reactions. The study was carried out blind under Workshop conditions and the results confirm the method as an accurate means of determining HLA-A locus tissue types.

Null alleles of the aldolase B gene in patients with hereditary fructose intolerance

We report three new mutations in the gene for aldolase B that are associated with hereditary fructose intolerance (HFI). Two nonsense mutations create opal termination codons: R3op (C-->T, Arg3-->ter, exon 2) was found in homozygous form in four affected members of a large consanguineous Turkish pedigree and R59op (C-->T, Arg59-->ter, exon 3) was found on one allele in a woman of Austrian origin known to harbour one copy of the east European mutation, N334K (Asn334-->Lys). The third mutation occurred in a French HFI patient known to be heterozygous for the widespread mutation, A174D (Ala174-->Asp): a single mutation, G-->A, in the consensus acceptor site 3' of intron 6 was found on the remaining allele. These mutations are predicted to abrogate synthesis of functional protein and thus represent null alleles of aldolase B. The mutant alleles can be readily detected in the amplification refractory mutation system (ARMS) or (for R59op and 3' intron 6) by digestion of amplified genomic fragments with DdeI or A1wNI, respectively, to facilitate direct diagnosis of HFI by molecular analysis of aldolase B genes.

A simple method for detecting single base substitutions and its application to HLA-DPB1 typing

We have developed a simple and reliable method, PCR-PHFA (polymerase chain reaction dependent preferential homoduplex formation assay), for detection of single base substitutions within PCR amplicons. This technique is based upon strand competition during hybridization between a double labeled amplicon, prepared from biotin and DNP labeled primers, and an unlabeled amplicon. Under the precisely controlled temperature gradient, the preferential formation of a homoduplex over a heteroduplex occurs. After annealing, the identical sequence of the double labeled and unlabeled amplicon resulted in a low population of regenerated double labeled dsDNA due to strand exchange between them. Even when the two differed by only a single base substitution, double labeled molecule was regenerated efficiently because of preferential homoduplex formation. The regenerated double labeled molecule was captured onto a streptavidin coated microtiter plate and quantified enzymatically with a chromogenic substrate. The technique has been successfully applied in HLA-DPB1 typing. Furthermore, we detected a mutated gene even in the presence of a large excess of the corresponding normal gene.

TGGE and HIEF: a comparison of two methods in the detection of carriers of the Z mutation in the alpha-1-antitrypsin gene

Alpha-1-antitrypsin (alpha-1-AT) deficiency can lead to juvenile liver cirrhosis and lung emphysema in adulthood. The deficiency Z allele is caused by a base transition. Temperature gradient gel electrophoresis (TGGE) and hybrid isoelectric focusing (HIEF) were used to detect carriers of the Z mutation of the alpha-1-AT gene. The resulting data were compared. To verify carriers at the sequence level, a manual nonradioactive sequencing strategy was established. Among our sample of carriers of the Z mutation, two were not detected by HIEF that could be identified by TGGE. DNA of all TGGE identified individuals harboring the Z mutation of the alpha-1-AT gene were sequenced nonradioactively. All carriers harbored a G to A transition at position 11.940. This mutation is described to cause the altered protein.

Novel cystic fibrosis mutation associated with mild disease in Cypriot patients

Cyprus is an island in the eastern Mediterranean basin inhabited by people of Caucasian extraction, mostly Greek-Cypriots. The most common inherited disease among Caucasians is cystic fibrosis (CF). Although no careful scientific study had ever been done the impression was that CF was extremely rare among the Greek-Cypriots, with an incidence estimated at around 1:30,000. About 2 years ago, we introduced molecular diagnostic methodology in an effort to assist clinicians in safer diagnosis of patients presenting with atypical CF symptomatology, and also for testing the hypothesis that mutations that cause milder phenotypes might be responsible for misdiagnosis or for missing entirely some cases of CF. Initial screening for delta F508 revealed that it is indeed rare in the general population. Further screening of suspected CF patients revealed a novel mutation that converted leucine at position 346 to proline (L346P) in two unrelated families. The second CF mutation was delta F508 and 1677delTA in the two families respectively, both reportedly associated with severe phenotypes. Yet our patients did not present with typical CF pictures possibly because of the dominant nature of this novel mild mutation in exon 7. Symptoms included failure to thrive, chest infections and electrolyte disturbances. These findings raise the possibility that Cyprus might have been spared very severe CF phenotypes but not cystic fibrosis transmembrane conductance regulator (CFTR) mutations.

Association of TAP2 polymorphism with rheumatoid arthritis is secondary to allelic association with HLA-DRB1

OBJECTIVE

To study polymorphisms of the newly described TAP2 locus in rheumatoid arthritis (RA) and to analyze their relationship with HLA-DRB1 alleles previously implicated in the development of the disease.

METHODS

TAP2 polymorphic residues at 3 sites, Val/Ile-379, Ala/Thr-565, and Ala/Thr-665, were characterized by amplification refractory mutation system polymerase chain reaction in 185 RA patients and 48 HLA-DR4 positive healthy controls. HLA-DR4 subtypes were determined by sequence-specific priming and oligonucleotide hybridization.

RESULTS

The frequencies of Ile-379, Thr-565, and Thr-665 were significantly increased in DR4 positive versus DR4 negative RA patients. TAP2 genotype distributions also differed between the patient groups stratified by DR4 status. However, no significant differences in TAP2 polymorphisms were observed between DR4 positive RA patients and DR4 positive controls, although relationships between specific DR4 subtypes and TAP2 variants were identified.

CONCLUSION

Particular TAP2 polymorphisms are associated with distinct HLA-DR specificities in both normal and RA populations. Thus, the prevalence of specific TAP2 residues and genotypes in RA appears to be secondary to the HLA-DR frequencies and genotypic combinations that are typical of RA.

Molecular analysis of C3 allotypes in Chinese patients with immunoglobulin A nephropathy

The third component of complement (C3) exists in two main allotypic forms, C3S and C3F. An increased frequency of the rarer C3F allele has been reported in several autoimmune conditions, including immunoglobulin A nephropathy (IgAN), in white patients. C3F is known to be rare in the Chinese population, but C3 allotypes have not been studied in Chinese patients with IgAN. The molecular basis of the S/F polymorphism has been established recently: a single base change at the DNA level encodes a single amino acid substitution in the protein. A second polymorphism, closely linked to the first, is defined by the monoclonal antibody HAV 4-1, and also is due to a single base change. These polymorphisms therefore can be analyzed at the DNA level. We have used the amplification refractory mutation system, a modification of the polymerase chain reaction, to analyze these two C3 polymorphisms on genomic DNA from 133 Hong Kong Chinese individuals: 54 patients with IgAN and 79 controls. No C3F alleles were present in either group: all individuals were homozygous C3S. Twenty-six patients were also allotyped for the HAV 4-1 polymorphism; all 26 were homozygous HAV 4-1 negative, as would be predicted from the close linkage of this allotype to C3S in other populations. These data indicate that C3F is not a susceptibility allele for IgAN in Hong Kong Chinese individuals, and confirm in a large DNA-based study the rarity of C3F in this population.

Analysis of polymerase chain reaction product by capillary electrophoresis and its application to the detection of single base substitution in genes

Capillary gel electrophoresis (CGE) was studied for the direct analysis of polymerase chain reaction (PCR) amplified samples. A low cross-linked polyacrylamide gel (3%T, 0.5%C) was used for CGE with treated and untreated silica capillaries. CGE showed high reproducibility and resolution in the separation of DNA fragments (ca. 100-1000 base pairs) produced by PCR. The CGE system was applied to the detection of an amplification refractory mutation system (ARMS) and PCR-restriction fragment length polymorphism (PCR-RFLP), which are detection methods of single base substitution in genes using PCR. With the CGE system, full automation of PCR product detection is feasible.

Search for mutations in the beta 1 GABAA receptor subunit gene in patients with schizophrenia

As alterations in GABAergic neurotransmission have been indirectly implicated in the pathogenetics of schizophrenia, GABAA receptor subunit genes are plausible candidate genes for the illness. We undertook a search for sequence variations in the coding region of beta 1 subunit gene by designing intron-based primers to amplify its 9 exons. Using single strand conformation polymorphism (SSCP) analysis, we found an exon 9 variant present in 3 of 86 unrelated schizophrenic cases derived from families having at least 2 first-degree relatives with schizophrenia. Direct sequencing of the SSCP variant revealed a C-->G nucleotide transversion at codon 396 predicting a histidine to glutamine substitution in the beta 1 peptide. The predicted amino acid substitution occurs at a highly conserved site, 9 residues from a cAMP-dependent serine phosphorylation consensus sequence. All known GABAA beta 1 subunit genes including human, bovine, and rat, code for histidine at position 396. Although the variant cosegregated with disease in a family with 2 affected sibs, it was only transmitted to 2 of 3 affected sibs in a multiplex family. The variant was not found in an additional sample comprising 155 unrelated schizophrenics and the sequence variant was present at a low frequency (approximately 1.1%) in control groups. Although these results indicate that the sequence variant is likely to be a natural polymorphism, it is possible that the variant may be a predisposing allele in rare instances. It is also possible that the variant may change the function or regulation of the GABAA receptor complex and it may be of pharmacogenetic relevance.

Molecular and population genetic analysis of allelic sequence diversity at the human beta-globin locus

Allelic sequence polymorphism at the beta-globin locus was investigated in a group of 36 Melanesians. A 3-kilobase fragment containing the gene and its flanking regions was sequenced in 60 normal (beta A) and 12 thalassemic (intron 1, position 5, G-->C) chromosomes. Haplotype relationships between linked polymorphisms were derived by allele-specific PCR amplification and sequencing. Seventeen nucleotide polymorphisms and 2 length variants were identified, and these sites segregated as 17 sequence haplotypes in the normal chromosomes. This haplotype diversity is higher than that expected on the basis of the nucleotide polymorphism observed and is probably due to recombination and gene conversion. Nucleotide diversity at synonymous sites in the sample is 0.14%, suggesting an average age of sequence divergence of approximately 450,000 years, consistent with that expected for a neutrally evolving human nuclear locus.

A PCR based method to determine the Kalow allele of the cholinesterase gene: the E1k allele frequency and its significance in the normal population

The Kalow allele for cholinesterase is a quantitative variant of the usual gene and has been shown to result from a single base pair change in the DNA. A new method based on the polymerase chain reaction to distinguish Kalow alleles of the cholinesterase gene was developed. Using the amplification refractory mutagenesis system, two different reactions distinguished the presence of a guanine (normal E1u allele) from that of an adenine (Kalow E1k allele) at nucleotide 1615 within the coding sequences of the gene. The frequency of the Kalow allele in our sample of 51 persons was determined to be 20%. The mean total cholinesterase activity in heterozygotes was 90% of that in persons who typed as E1uE1u homozygotes. Two E1kE1k homozygotes were identified and their cholinesterase activities were the two lowest measured.

Type-specific amplification of viral DNA using touchdown and hot start PCR

Two types of JC virus (JCV) are found in infected brain and kidney tissues. A highly reliable PCR assay to determine viral type in tissue is presented. This type-specific system is analogous to allele-specific PCR used to detect point mutations in cellular genes. Specific amplification of two fragments, using four pairs of type-specific primers, is based on a single nucleotide difference at the 3'-ends of the primers. A combination of three conditions in the PCR reaction was required for specificity: 'hot start', a ramped ('touchdown') cycle profile, and a slightly lowered molar concentration of the specific primers and dNTPs. Efficient yield of PCR product is not lost under these conditions, and even the least selective mismatches (C:A and T:G) provided specific amplification. Type-specific restriction enzyme sites within the amplified fragments confirm type designation.

Hepatitis B virus precore mutation and fulminant hepatitis in the United States. A polymerase chain reaction-based assay for the detection of specific mutation

Hepatitis B virus (HBV) variants with precore mutation(s) resulting in the absence of HBeAg production have been associated with the occurrence of fulminant hepatitis in Japan, Israel, and southern Europe, where the prevalence of this HBV strain appears common. In areas such as United States, where HBV infection is not endemic, the role of this mutant virus in fulminant hepatitis is unknown. We developed an amplification refractory mutation detection system to detect specifically the presence of the G to A mutation at nucleotide position 1898, which is the most frequently observed mutation resulting in a precore stop codon. In addition, this method provided a quantitative measurement of the relative ratio of one strain to the other. Using this system, we tested HBV strains for the presence of the stop codon mutation in sera from 40 cases of fulminant hepatitis B occurring in the United States. Serum HBV DNAs from 28 patients were analyzed successfully. A mixture of wild-type and mutant strains in various ratios were observed in 15 patients, wild type exclusively in 11, and mutant exclusively in 2. Four of these patients had undergone liver transplantation for HBV-associated cirrhosis and developed fulminant HBV-associated hepatitis after transplantation. Pre- and posttransplant serum samples from one patient were analyzed: a mixture of wild-type and mutant HBV strains was detected in both samples. Our study demonstrated that both wild-type and mutant HBV strains are associated with fulminant hepatitis, and that in some patients in the United States, factors other than precore mutations contribute to the development of fulminant hepatitis.

Two new mutations in the porphobilinogen deaminase gene and a screening method using PCR amplification of specific alleles

Acute intermittent porphyria (AIP) is attributable to defects in the porphobilinogen deaminase (PBGD) gene. Two new mutations have been found in the PBGD gene in Swedish families. The first is a G to A splice mutation in the last position of intron 9. A screening method using allele-specific amplification has been designed for the rapid detection of this mutation. The second mutation is a C to T substitution in exon 10, changing Arg201 to Trp. This mutation can be detected by restriction enzyme cleavage.

A robotics-assisted procedure for large scale cystic fibrosis mutation analysis

We describe a convenient, efficient, semiautomated protocol for assaying large numbers of DNA samples for over 20 mutations causing cystic fibrosis. The protocol uses the following: (1) a programmable robotic workstation to perform rapid pipetting and dot-blotting operations, (2) an allele-specific oligonucleotide hybridization in a single water bath without correcting for G+C content of oligonucleotides, and (3) a combinatorial system that allows direct determination of the genotype for more frequent mutations. We have used this system routinely for 16 months for carrier detection and for diagnosis of cystic fibrosis. The method can be readily applied to any combination of allele-specific oligonucleotide assays whether for multiple alleles at one locus or for a few alleles at multiple loci.

Detection of point mutations by solid-phase methods

Several techniques exist that permit the efficient distinction among characterized DNA sequence variants. In this review we discuss a number of such analytic procedures. These techniques all take advantage of a variety solid supports to prepare and analyze reaction products. The described diagnostic principles are now being applied for the development of miniaturized assay formats, suitable for automated detection of large sets of sequences in clinical samples.

Associations between alleles of the major histocompatibility complex-encoded ABC transporter gene TAP2, HLA class II alleles, and celiac disease susceptibility

The study of celiac disease among Southern European populations has confirmed the hypothesis from Northern Europe that a close association exists between disease susceptibility and a combination of polymorphic alleles at the HLA-DQ loci (DQA1*0501-DQB1*0201) arranged either in a cis- or a trans-configuration. Attempts to identify additional genetic influences have been inconclusive, although many studies have raised possibilities of further major histocompatibility complex (MHC)-linked susceptibility genes. This study examines the disease associations of polymorphisms of a recently discovered gene located close to the DQ loci, TAP2, whose products are thought to be involved in the transport of antigen peptides across the endoplasmic reticulum for binding to HLA class I molecules. Like the products of the DQ loci, the product of TAP2 forms part of a heterodimeric molecule with products of a second genetic locus, TAP1, which is located centromerically to TAP2. The populations studied were central Italians from Rome and Ashkenazi Jews from Rehovot, Israel. HLA studies demonstrate that the Roman celiac group has a high proportion of people with DR3-negative celiac disease in whom the combination DR5/7 is frequently found. In Israel, 20% of celiac patients lack the DQ susceptibility markers but are DR4 positive. The polymorphic substitutions of TAP2 studied encode amino acid changes in the trans-membrane region (position 379) and the ATP-binding cassette region (positions 565 and 665) of the protein. No TAP2-specific disease associations were found in any HLA subgroup.(ABSTRACT TRUNCATED AT 250 WORDS)

PCR assays of variable nucleotide sites for identification of conservation units

A number of authors have recently suggested that the best approach for identifying units of conservation is to follow a systematics model of character analysis (Amato, 1991; Cracraft, 1991; Vogler and DeSalle, 1994). This approach necessitates the use of an operational, typological, evolutionary species concept. The use of the phylogenetic species concept has the utility and philosophical logic appropriate for this task. Additionally, there is a large body of literature that uses this framework, along with a parsimony based character analysis to identify patterns of phylogeny (Cracraft, 1983; Nelson and Platnick, 1981; Nixon and Wheeler, 1990). While we advocate this approach, we recognize that one of its limiting factors is sample size. We propose that by selective direct sequencing plus rapid sampling of variable target characters by polymerase chain reaction (PCR) assays of specific sites, sufficiently large numbers of individuals can be accurately, inexpensively, and quickly surveyed for diagnostic characters. This procedure is demonstrated by a survey of variable nucleotide sites in the Caiman crocodilus complex.

Intron splice acceptor site sequence variation in the hereditary non-polyposis colorectal cancer gene hMSH2

Common but weakly penetrant mutations of certain genes may confer an increased susceptibility to colorectal cancer and account for a proportion of 'sporadic' cases. We analysed DNA from 111 colorectal cancer cases and 114 controls for a specific candidate sequence variation in the hereditary non-polyposis colorectal cancer gene hMSH2. The variant sequence was found in a quarter of individuals, and there was no difference between cancer cases and controls, according to age of development of cancer or presence of family history. It thus appears that this particular sequence variation is a polymorphism rather than a mutation which increases cancer susceptibility.

Rapid HLA typing by multiplex amplification refractory mutation system

AIMS

To detect HLA susceptibility and protective alleles associated with insulin dependent diabetes mellitus (IDDM) using a multiplex amplification refractory mutation system (ARMS). These include DR3 and DR4 alleles at the DRB1 locus, presence or absence of aspartic acid at position 57 (Asp-57) of the DQB1 locus, and presence or absence of arginine at position 52 (Arg-52) of the DQA1 locus.

METHODS

The ARMS approach was used to design allele specific primers for the detection of the major susceptibility and protective alleles for IDDM. These include DR3 and DR4 alleles at the DRB1 locus, Asp-57 and non-Asp-57 at the DQB1 locus, and Arg-52 and non-Arg-52 alleles at the DQA1 locus. The allele specificity of each set of primers was first tested separately using DNA samples from 15 individuals previously typed for the DRB1, DQB1, and DQA1 loci using the sequence specific oligonucleotide (SSO) technique. The possibility of using multiplex ARMS for typing multiple susceptibility/protective alleles for IDDM was further investigated by testing various combinations of allele specific primers, thereby reducing the number of separate polymerase chain reactions required to type all these alleles.

RESULTS

A "three-tube" system worked well and gave accurate results. Tube 1 contained ARMS primers for the detection of IDDM susceptibility alleles DR3 and DR4; tube 2 contained ARMS primers for the detection of susceptibility alleles non-Asp-57 and Arg-52; and tube 3 contained ARMS primers for the detection of the protective alleles Asp-57 and non-Arg-52. DNA samples typed with this ARMS method were in complete agreement with those obtained using the SSO technique.

CONCLUSION

This method is rapid and has no requirement for radioactivity. It is an efficient method for population screening.

Direct genotyping and prenatal diagnosis of beta-thalassemia in Chinese by polymerase chain reaction mediated restriction fragment length polymorphism method

The molecular basis of beta-thalassemia is predominantly point mutations in the beta-globin gene. Frameshift 41-42 (-CTTT), IVS-2 position 654 (C-->T) mutation, nonsense codon 17 (A-->T), TATA box position -28 (A-->G) mutation and frameshift 71-72 (+A) account for more than 95% of beta-thalassemia alleles in the population of South China. We have developed a polymerase chain reaction (PCR)-mediated restriction fragment length polymorphism (RFLP) method for the identification of these alleles. In this method, artificial mispairing bases in PCR-amplified products were created to distinguish normal from mutant alleles on the basis of RFLPs. The size of the five PCR-amplified DNA fragments that may potentially contain the above five types of mutations is 93 or 89 bp (codons 41-42), 221 bp (IVS-2 nt 654), 110 bp (codon 17), 123 bp (TATA box nt -28), and 97 or 98 bp (codons 71-72). After these fragments were digested with Hinc II, Mae III, Nhe I, EcoR I, and Dde I, respectively, the allele-specific RFLPs produced were analyzed by gel electrophoresis. DNA samples of 24 patients with the above five types of beta-thalassemia were investigated with the present method and allele-specific oligonucleotide (ASO) probing simultaneously. We used this method in the prenatal diagnosis of 14 Chinese families for beta-thalassemia. The results obtained by the present method correspond well with those by the ASO probe test.

HLA-DPB1 glutamate 69: a genetic marker of beryllium disease

Chronic beryllium disease (CBD) is a lung disorder related to beryllium exposure and is characterized by the accumulation in the lung of beryllium-specific CD4+ major histocompatibility complex (MHC) class II-restricted T lymphocytes. Evaluation of MHC class II genes in 33 CBD cases and 44 controls has shown a negative association with HLA-DPB1*0401 (P < 0.001) and a positive association with HLA-DPB1*0201 (P < 0.05) alleles, which differ at residues 36, 55 to 56, and 69 of the beta 1 chain. Among CBD cases, 97 percent expressed the HLA-DPB1*0201-associated glutamic acid (unaffected population, 30 percent; P < 0.001) at residue 69, a position involved in susceptibility to autoimmune disorders. This suggests that HLA-DP has a role in conferring susceptibility and that residue 69 of HLA-DPB1 could be used in risk assessment for CBD.

Allele-specific amplification for the identification of several hemoglobin variants

Eight known abnormal hemoglobins in more than 40 patients have been identified with an allele-specific amplification procedure. These are mutants of the A gamma (Hb F-Sardinia), the delta (Hb B2), the alpha (Hb G-Philadelphia), and the beta (Hbs S, C, E, D-Los Angeles, O-Arab) globin genes. Adjustment to an unusually high annealing temperature improves the procedure greatly, allowing excellent discrimination between normal and mutant alleles, irrespective of the particular mismatch. The discrimination includes the Hbs C and E in the same reaction mixture-multiplex allele-specific amplification. The procedure can successively use primers with 3'-penultimate critical nucleotides, degenerative ends, and potentially dimerizing properties.

Single-step allele-specific polymerase chain reaction HLA-DQ genotyping using ARMS primers

A set of allele-specific oligonucleotide primer pairs has been developed that allows the determination of HLA-DQ genotypes in a rapid, single-step PCR. The primer set unambiguously distinguishes the 18 most common DQ haplotypes in heterozygous as well as homozygous individuals. Because of linkage disequilibrium between the DQ and DR gene loci, accurate determination of the DQ haplotypes enables the prediction of the DR serotype. HLA-DQ genotyping can be performed using DNA from any tissue, such as skin and hair roots, as well as from blood cells. It is therefore anticipated that HLA-DQ genotyping by PCR will have applications in forensic science, in the identification of individuals, in research studies of the role of DQ and DR haplotypes in the pathogenesis of autoimmune diseases, and in the rapid matching of organ donor and transplant recipient pairs.

Detection of chimaerism after bone marrow transplantation using the double amplification refractory mutation system

We have developed a highly sensitive double amplification refractory mutation system (double ARMS) for the detection of extremely low levels of mixed chimaerism after bone marrow transplantation. The system we chose for double ARMS analysis is a highly polymorphic region 5' to the human delta-globin gene. Double ARMS analysis was found to correlate well with an established minisatellite system and was shown to demonstrate a very low level of mixed chimaerism in cases undetectable by the latter method.

Hemoglobin E and codon 17 nonsense: two beta-globin gene mutations common in Southeast Asia detected by the use of ARMS

Hemoglobin E (codon 26 GAG-->AAG) and codon 17 nonsense (AAG-->TAG), two clinically important mutations of the beta-globin gene, are common in Southeast Asia. The detection of these mutations using allele-specific PCR is described. Together with the previously reported method for the detection of the common Southeast asian codon 41-42 frameshift mutation (del CTTT), it is possible to identify the vast majority of clinically important beta-globin gene mutations in Southeast Asian populations by means of nonradioactive methods.

A simple and efficient method for site-directed mutagenesis with double-stranded plasmid DNA

A general, simple and efficient method for preparing site-specific mutations in double-stranded plasmid DNA without the need for special plasmids, bacterial strains or reagents is described. Only one synthetic oligonucleotide for each mutation is required, subcloning is unnecessary and a high efficiency of mutation (58-97%) was obtained. If two synthetic oligonucleotide primers are used, two separate mutations can be simultaneously created in a single reaction tube.

Mutagenically separated PCR (MS-PCR): a highly specific one step procedure for easy mutation detection

With increasing knowledge about the causal role of genetic defects in clinical diseases the necessity is apparent to have procedures for rapid diagnosis of point mutations. We developed a PCR-based technique, whereby both normal and mutant alleles can be amplified in the same reaction tube, using different length allele-specific primers. Furthermore the allele-specific primers introduce additional deliberate differences into the allelic PCR-products that drastically reduce crossreactions in subsequent cycles. This mutagenesis separates the amplification reactions of the alleles performed in the same tube. Subsequent identification of the PCR-products is done by gel electrophoresis and shows at least one of the two allelic products. Therefore, in addition to simple handling, MS-PCR provides a within-assay quality control for the exclusion of false negative results. The feasibility of this technique has been tested using six different mutations. The high sensitivity of MS-PCR also allows screening for mutation carriers in pooled DNA samples.

Defining the common subtypes of HLA A9, A10, A28 and A19 by use of ARMS/PCR

We describe sequence-specific primer (SSP) combinations for use in a one-step polymerase chain reaction (PCR) typing system to determine HLA-A locus subtypes of A9 (A23, A24), A10 (A25, A26, A43), A28 (A*6801, A*6802, A*6901) and A19 (A*2901, A*2902, A*3001, A*3002, A31, A32, A33) from genomic DNA. SSP's were designed on the basis of the amplification refractory mutation system (ARMS) in which a mismatch at the 3' residue inhibits non-specific amplification. The SSP combinations described extend our low-resolution typing system, to provide a high-definition typing of the HLA-A locus.

An antigen processing polymorphism revealed by HLA-B8-restricted cytotoxic T lymphocytes which does not correlate with TAP gene polymorphism

In previous studies of antigen presentation through HLA-B27, we identified a healthy person whose lymphoblastoid cells do not present three B27-restricted viral epitopes to specific cytotoxic T lymphocytes (CTL), despite adequate cell surface expression of HLA-B2702 of normal sequence. Similar findings were observed in all members of his family sharing the HLA-A3-B2702 haplotype. The original donor, NW, carries HLA-B8 on his other class I haplotype, which his daughter, HW, has inherited. We now report a failure to present an HLA-B8-restricted epitope from influenza nucleoprotein following viral infection of NW cells, although exogenous added peptide is still presented normally. However, cells from HW, which do not carry the A3-B2702 haplotype, present the expected epitope after viral infection. Another B8-restricted epitope, from human immunodeficiency virus-gag, is presented equally well by both cell lines when infected with gag-vaccinia. This antigen processing phenotype does not correlate with any of the known human TAP-1 and TAP-2 polymorphisms.

Strong association between polymorphisms in an intronic microsatellite and in the coding sequence of the BoLA-DRB3 gene: implications for microsatellite stability and PCR-based DRB3 typing

A highly polymorphic microsatellite in the bovine DRB3 gene was characterized by polymerase chain reaction (PCR) analysis and DNA sequencing. A very strong association between expressed DRB3 polymorphism and microsatellite alleles was revealed by PCR analysis of genomic DNA from 116 animals representing three breeds of cattle. The results indicated a low frequency of microsatellite length mutations as the association was consistent over breeds. The DRB3 microsatellite may be utilized in a PCR-based typing method of bovine class II alleles. The microsatellite polymorphism did not distinguish all known DRB3 alleles, but it was shown that this method may be complemented by the use of allele-specific PCR based on the extensive polymorphism in the DRB3 exon 2. The DNA sequences of seven microsatellite alleles, associated with different class II haplotypes, were determined. The DRB3 microsatellite is composed of three repeat motifs, a stretch of at least 10 uninterrupted (TG)n dinucleotides, a long but interrupted stretch of (GA)n dinucleotides, and a few (CAGA)n tetranucleotides. There were pronounced sequence differences between alleles and the results indicated that the evolution of this microsatellite has involved length mutations of the dinucleotide repeats as well as point mutations causing interruptions in the dinucleotide repeats.

Apolipoprotein E phenotypes and genotypes as determined by polymerase chain reaction using allele-specific oligonucleotide probes and the amplification refractory mutation system in children with insulin-dependent diabetes mellitus

The frequency of apolipoprotein E (apo E) phenotypes and genotypes due to allelic variation at amino acids 112 and 158 was analysed in 50 children with type I diabetes. Phenotypes were determined by isoelectric focusing and genotypes by the technique of polymerase chain reaction using allele-specific oligonucleotide probes (PCR/ASO) and the amplification refractory mutation system (ARMS). Discrepancies between phenotypes and genotypes as assigned by PCR/ASO were observed in 12 (24%) cases and by ARMS in eight (16%) cases. Results revealed the apo E3/3 genotype, as assigned by ARMS, to be the most frequent one (70%), followed by apo E3/4 in 16%, apo E2/2 in 2%, apo E2/3 in 8%, apo E2/4 in 2% and apo E4/4 in 2% of the cases. Apo E3/4 genotype and phenotype were more frequently present in the children with type I diabetes as compared with the diabetic adults previously reported on.

PCR amplification of specific alleles: rapid detection of known mutations and polymorphisms

We review a method termed PCR Amplification of Specific Alleles (PASA), a generally applicable technique for the detection of known point mutations, small deletions and insertions, polymorphisms and other sequence variations. PASA is a modification of PCR that depends on the synthesis of a PCR oligonucleotide primer that precisely matches with one of the alleles but mismatches with the other. When the mismatch occurs near the 3' end of the PCR primer, amplification is inefficient. Therefore, preferential amplification of the perfectly matched allele is obtained. The method should be generally applicable as our results indicate that with proper optimization all possible alleles can be reliably distinguished. The ease and technical simplicity of PASA make genetic analyses more accessible. PASA can be also adapted to accommodate specific requirements and can be extended by incorporating other techniques. Moreover, PASA shows promise for population screening because the technique is rapid, highly reproducible, inexpensive, nonisotopic, and amendable to automation.

Mutation-specific PCR: a rapid and inexpensive diagnostic method, as exemplified by mitochondrial DNA analysis in Leber's hereditary optic neuropathy

Mitochondrial DNA analyses were carried out on 30 individuals with clinically documented or suspected Leber's hereditary optic neuropathy (LHON). Three methods based on the polymerase chain reaction (PCR) were compared, all three aiming at detecting the G/C to A/T mutation of base pair 11,778 causing LHON. Two methods included restriction analysis with either Sfa NI or Mae III, while the third one relied on allele-specific amplification (ASA), using a mutation-specific primer. The results were completely consistent, showing the presence of the mutation in 18 and its absence in 12 cases. From these results it is concluded, that mutation-specific PCR is the diagnostic method of choice, because it obviates the need for subsequent restriction analysis, thus being faster and more cost-efficient. The general applicability of ASA makes this strategy universally useful for detection of specific mutations in the diagnostic analysis of genetic disease, and for typing of genetic polymorphisms or other sequence variations due to single-base differences.

Multiplex ARMS-RFLP: a simple and rapid method for HLA-DR4 subtyping

We have developed a simple and rapid non-radioactive technique for HLA-DR4 subtyping. A multiplex ARMS-RFLP (Amplification Refractory Mutation System--Restriction Fragment Length Polymorphism) system allows HLA-DR4 subtyping by analysis of the products of two multiplex ARMS reaction mixtures. For some cases, restriction enzyme digests (Hae II and/or SacII) of the products are analysed. The technique relies on the fact that an ARMS primer with a mismatch at its 3'-end with respect to the template will not be elongated under PCR conditions. Hence, by designing ARMS primers such that different HLA-DR4 alleles yield PCR products of different lengths, only two reactions, each using a mixture of different ARMS primers, are sufficient to type all of the known HLA-DR4 alleles. This system can distinguish between HLA-DR4 'homozygotes' and 'heterozygotes' since every HLA-DR4 allele can be detected. The ARMS conditions were optimized using DNA from cell lines. This technique has now been used to type a panel of rheumatoid arthritis patients and controls.

Estimation of the incidence of a rare genetic disease through a two-tier mutation survey

Recent attempts to detect mutations involving single base changes or small deletions that are specific to genetic diseases provide an opportunity to develop a two-tier mutation-screening program through which incidence of rare genetic disorders and gene carriers may be precisely estimated. A two-tier survey consists of mutation screening in a sample of patients with specific genetic disorders and in a second sample of newborns from the same population in which mutation frequency is evaluated. We provide the statistical basis for evaluating the incidence of affected and gene carriers in such two-tier mutation-screening surveys, from which the precision of the estimates is derived. Sample-size requirements of such two-tier mutation-screening surveys are evaluated. Considering examples of cystic fibrosis (CF) and medium-chain acyl-CoA dehydrogenase deficiency (MCAD), the two most frequent autosomal recessive disease in Caucasian populations and the two most frequent mutations (delta F508 and G985) that occur on these disease allele-bearing chromosomes, we show that, with 50-100 patients and a 20-fold larger sample of newborns screened for these mutations, the incidence of such diseases and their gene carriers in a population may be quite reliably estimated. The theory developed here is also applicable to rare autosomal dominant diseases for which disease-specific mutations are found.

Detecting single-base mutations

The ability to detect single-base changes is of fundamental importance in molecular genetics. This is particularly true in human genetics, where interest in linking mutations of identified genes to particular disease phenotypes is most intense, and where a demand exists for clinical diagnosis of defined mutations. In the following article, techniques are described for screening unknown mutations, as well as diagnosing those that have been identified previously. The underlying methods are explained briefly and guidelines are offered for choosing one technique in preference to another.

Novel association approach for determining the genetic predisposition to schizophrenia: case-control resource and testing of a candidate gene

We have developed a two-tiered approach to elucidating the genetic predisposition to schizophrenia. The approach first involves the examination of candidate genes in a subset of schizophrenic individuals to identify DNA sequence variations of likely functional significance, i.e., that produce either structural alterations in the protein or affect the level of gene expression. Once identified, the prevalence of the aberrant allele is examined in a large group of unrelated schizophrenic cases and controls to assess whether a true disease association exists. Herein, we describe the establishment of a DNA bank on nearly 200 unrelated schizophrenic cases defined by DSM-III-R criteria and on over 300 unrelated, ethnically similar controls. Characteristics of the study sample are described. The study approach then is illustrated by testing known mutations in the phenylalanine hydroxylase gene, responsible for the autosomal recessive disease of phenylketonuria, in the case-control sample to determine if carriership of a mutant allele is associated with an increased risk of schizophrenia. Using PCR amplification of specific alleles (PASA), we screened 190 schizophrenic cases and 336 controls for two common point mutations in the phenylalanine hydroxylase gene. Two carriers were found among the controls, while none of the cases was shown to carry a mutant allele. Thus, carriership of either of two common mutations in the phenylalanine hydroxylase gene does not appear to be associated with an increased risk of schizophrenia. As additional candidate genes are tested in this case-control resource, adjustment for multiple comparisons will become crucial in order to reduce the chance of false positive findings.(ABSTRACT TRUNCATED AT 250 WORDS)

Highly lytic CD8+, alpha beta T-cell receptor cytotoxic T cells with major histocompatibility complex (MHC) class I antigen-directed cytotoxicity in beta 2-microglobulin, MHC class I-deficient mice

Targeted disruption of the beta 2-microglobulin (beta 2m) gene results in major histocompatibility complex (MHC) class I deficiency and virtual disappearance of functional CD8+ cytotoxic T lymphocytes (CTLs) in beta 2m-deficient (beta 2m-/-) mice. We asked whether the beta 2m-/- mice are able to reject tumor cells injected i.p. and what is the cellular composition of peritoneal exudate leukocytes (PELs) from such mice. We found that beta 2m-/- mice do reject MHC class I-bearing tumor cells injected i.p. Surprisingly, analysis of PEL CTLs obtained from i.p. tumor-injected beta 2m -/- mice revealed the presence of a large proportion of functional, tumor-destroying CD8+, CD4-, alpha beta T-cell receptor-positive, CD3+, Thy-1+, MHC class I-negative CTLs with strong MHC class I-directed cytotoxic activity. These results call for careful studies of local accumulation of CD8+ CTLs in beta 2m -/- mouse models and suggest that the dramatic decrease in MHC class I expression caused by beta 2m gene disruption does not prevent CD8+/CD4- cell selection and expansion.